plot_uncertainty: Uncertainty of the peptide measurements

In HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Uncertainty of the peptide measurements

Description

Plot the uncertainty of the mass measurements - for aggregated data or before aggregation - to see if there is a region with uncertainty higher than acceptable

Usage

plot_uncertainty(
  dat,
  protein = dat[["Protein"]][1],
  state = dat[["State"]][1],
  skip_amino = 0,
  aggregated = TRUE,
  separate_times = TRUE,
  show_threshold = TRUE,
  interactive = getOption("hadex_use_interactive_plots")
)

Arguments

dat	data imported by the read_hdx function
protein	selected protein
state	selected biological state for given protein
skip_amino	integer, indicator how many amino acids from the N-terminus should be omitted
aggregated	logical, indicator if presented data is aggregated on replicate level
separate_times	logical, indicator if the values for different time points are presented separately
show_threshold	logical, indicator if the threshold of significance is shown
interactive	logical, whether plot should have an interactive layer created with with ggiraph, which would add tooltips to the plot in an interactive display (HTML/Markdown documents or shiny app)

Details

The function plot_uncertainty generates a plot of uncertainty of mass measurement of each peptide from selected protein in selected biological state. The values can be presented in two ways: as aggregated values for each replicate, or before aggregation - measured values for charge values within a replicate. On X-axis there is a position in a sequence, with length of a segment of each peptide representing its length. On Y-axis there is uncertainty of the measurement in Daltons. The threshold is set to 1 Da, as this value is associated with exchange.

Value

a ggplot object.

See Also

read_hdx calculate_exp_masses

Examples

plot_uncertainty(alpha_dat)
plot_uncertainty(alpha_dat, aggregated = FALSE)
plot_uncertainty(alpha_dat, aggregated = FALSE, separate_times = FALSE)
plot_uncertainty(alpha_dat, skip_amino = 1)

HaDeX2 documentation built on Feb. 9, 2026, 5:07 p.m.